Molecular Modelling - Innovation Lab 2020

Molecular dynamics-based investigation of interactions between Remdesivir analogue GS-441524 and a model human cell membrane using LAMMPS     As a case study for the Innovation Lab project we have decided to explore a topic somewhat related to the ongoing COVID-19 Pandemic. This said, in  the current race against SARS-CoV-2, interest has been drawn to Remdesivir, an antiviral approved for emergency treatment of COVID-19 in many countries. Remdesivir is a prodrug to the pharmacologically active GS-441524 and it transforms into the latter promptly after reaching the bloodstream (Scavone et al., 2020).      The purpose of this project was to predict whether GS-441524 is capable of entering a typical human cell, namely the cell of a lung wall. Since GS-441524 is a relatively hydrophilic molecule structurally resembling adenosine, we hypothesised that it might enter human cells through nucleoside transporters. To be more precise, through the human Equilibrative ...

 For a comprehensive guide on errors which may arise when running a simulation, click here .

To run a simulation in LAMMPS, both the input and data files must be placed in the same folder, and a terminal tab/command prompt in that particular folder must be invoked. Then, a correct LAMMPS simulation start-up command must be entered. The overall process to achieve this is similar in all operating systems, but there are certain differences.   For Windows users: 1.       Open the target folder. 2.       Click on the location bar in Windows Explorer. 3.       Type  cmd. 4.       Press  enter . 5.       Enter    mpiexec -np  [number of assigned processors]  lmp_mpi -in  [input file] mpiexec -np 4 lmp_mpi -in in.filename   For Mac users: 1.       Right click on the target folder. 2.       Hover over  services  in the right click menu. 3.   ...

  For a LAMMPS beginner, creating their first input file could be rather overwhelming. LAMMPS provides a vast array of commands with diverse applications, and it might be difficult to use them without any guidance. Nevertheless, the LAMMPS input file has some general structural requirements that are virtually unchanging for the majority of uses. To build a LAMMPS input file, the first step should be creating a plain text file. It is usually presented in the form in.filename. This document only includes some very common examples of LAMMPS commands. For a full command list,  see manual . Common structure: 1.       Main information about the system ·        Units. Available unit styles are  real ,  metal ,  si ,  csg ,  electron , and  micro.  For more information about the units command,  see manual . Correct format: units [unit style] units real ·        ...